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This study explored the effect of Ustilago esculenta infection on differentially expressed genes (DEGs) in male Manchurian wild rice (Zizania latifolia). We injected male Jiaobai plants at the five-leaf stage with U. esculenta suspension, and leaves at different timepoints after inoculation were collected for transcriptome sequencing. Transcriptome sequencing identified 1,226 DEGs mainly enriched in resistance-related processes. Weighted gene coexpression network analysis (WGCNA) showed that ‘plant–pathogen interaction’ and ‘MAPK signalling pathway-plant’ were the two most important upregulated pathways, and 16 candidate genes related to response to U. esculenta infection were screened. The results provide a basis for determining the molecular mechanisms of the response of male Z. latifolia to U. esculenta infection.